\documentclass[12pt]{nuthesis}	% The nuthesis class is based on 
				% amsbook.cls.
\usepackage{times,mathptmx}
\usepackage{amsfonts}
\usepackage{amsmath}

% Added by Tom
\newcommand{\sref}[1]{\S\ref{#1}} %for referencing sections
\newcommand{\fref}[1]{fig.~(\ref{#1})} %for referencing figures
\newcommand{\Fref}[1]{Fig.~(\ref{#1})} %for referencing figures
\newcommand{\frefp}[1]{figs.~(\ref{#1})} %for referencing figures
\newcommand{\Eqref}[1]{Eq.~(\ref{#1})} %for referencing equations
\newcommand{\Eqrefp}[1]{Eqs.~(\ref{#1})} %for referencing equations
\newcommand{\refb}[1]{(\ref{#1})} %ref with parenthesis

\newcommand{\abs}[1]{\lvert#1\rvert} %macros for abs and norm
\newcommand{\norm}[1]{\lVert#1\rVert}

%----acronym replacement
\newcommand{\ac}[1]{\textsc{#1}}
\newcommand{\acs}[1]{\textsc{#1}}
\newcommand{\acp}[1]{\textsc{#1}s}
\newcommand{\acl}[1]{{#1}}
\newcommand{\acf}[2]{{#1} (\textsc{#2})} %for first use (or complete use)
\newcommand{\acfp}[2]{{#1}s (\textsc{#2}s)}

\hyphenation{hyper-prior}

\newcommand{\ud}{\mathrm{d}} %roman 'd' in integrals etc.
\newcommand{\mat}[1]{{\bf{#1}}} %bold matrix
\newcommand{\vc}[1]{{\bf{#1}}} %bold vector
\newcommand{\vcg}[1]{{\boldsymbol{#1}}} %bold vector (greek character)
\newcommand{\hvc}[1]{\hat{\bf{#1}}} %for bold and hatted.

\newcommand{\ndist}[2]{\mathcal{N}\left(#1 \left|\,#2\right.\right)}   %normal distribution
\newcommand{\igdist}[2]{\mathcal{IG}\left(#1 \left|\,#2\right.\right)}   %inverse gamma distribution
\newcommand{\pdf}[1]{\p\left(#1 \right)}   %pdf
\newcommand{\cpdf}[2]{\p\left(#1 \left|\,#2\right.\right)}   %conditional pdf
\newcommand{\ndista}[2]{\mathcal{N}(#1 \mid #2)}   %normal distribution (variant)
\newcommand{\igdista}[2]{\mathcal{IG}(#1 \mid #2)}   %inverse gamma distribution
\newcommand{\cpdfa}[2]{\p(#1 \mid #2 )}   %conditional pdf (variant - smaller brackets)
\newcommand{\R}{\mathbb{R}}
\newcommand{\del}{\nabla} %grad operator


\newcommand{\E}[2]{\mathrm{E}_{#2}\left[#1 \right]} %expectation operator
\newcommand{\Ep}[2]{\mathrm{E}\left[#1 \right]_{#2}} %expectation operator (p at end)

\newcommand{\p}{{\mathrm p}}
\newcommand{\U}{{\mathrm U}}
\newcommand{\M}{{\mathrm M}}
\newcommand{\F}{{\mathrm F}}
\newcommand{\D}{{\mathrm D}}
\newcommand{\G}{{\mathrm {ND}}}
\newcommand{\T}{{\mathrm T}}
\newcommand{\I}{{\mathrm I}}
\newcommand{\g}{{\Gamma}}
\newcommand{\N}{{\cal N}}
\newcommand{\bE}{{\mathrm E}}
\newcommand{\varp}{\sigma_{\bf {\mathrm w}}^2}
\newcommand{\varn}{\sigma_{\bf {\mathrm n}}^2}
\newcommand{\balpha}{{\bm{\alpha}}}
\newcommand{\bbeta}{{\bm{\beta}}}
\newcommand{\bmode}{\mathbf{Mode}}
\newcommand{\blambda}{{\bm{\lambda}}}
\newcommand{\bmu}{{\bm{\mu}}}
\newcommand{\bpi}{{\bm{\pi}}}
\newcommand{\bOmega}{{\bm{\Omega}}}
\newcommand{\bomega}{{\bm{\omega}}}
\newcommand{\bGG}{{\bf GG}}
\newcommand{\bz}{{\bf z}}
\newcommand{\bx}{{\bf x}}
\newcommand{\by}{{\bf y}}
\newcommand{\bv}{{\bf v}}
\newcommand{\bu}{{\bf u}}
\newcommand{\bs}{{\bf f}}
\newcommand{\bh}{{\bf h}}
\newcommand{\bn}{{\bf n}}
\newcommand{\br}{{\bf r}}
\newcommand{\bg}{{\bf g}}
\newcommand{\bD}{{\bf D}}
\newcommand{\bB}{{\bf B}}
\newcommand{\bw}{{\bf w}}
\newcommand{\bC}{{\bf C}}
\newcommand{\bW}{{\bf W}}
\newcommand{\bN}{{\bf N}}
\newcommand{\bH}{{\bf H}}
\newcommand{\bY}{{\bf Y}}
\newcommand{\bX}{{\bf X}}
\newcommand{\bI}{{\bf I}}
\newcommand{\bM}{{\bf M}}
\newcommand{\bA}{{\bf A}}
\newcommand{\bl}{{\mathrm{bl}}}
\newcommand{\nhbr}{\,{\mathrm {nhbr}}\,}
\newcommand{\const}{{\mathrm {const}}}
\newcommand{\nn}{nn_i}
\newcommand{\bTV}{{\mathrm {TV}}}

%\newtheorem{pro}{Proposition.}
\newcommand{\bva}{{\mathrm {Var}}}
\newcommand{\bmo}{{\mathrm {Mode}}}

\usepackage{graphicx}
%\ifx\pdfoutput\undefined
%\usepackage{graphicx}
%\else
%\usepackage[pdftex]{graphicx}
%\if


\newcommand{\im}{{\mathrm{im}}}
\newtheorem{alg}{\noindent \textbf{Algorithm}}
\newcommand{\q}{{\mbox{q}}}

\def\argmax{\mathop{\rm argmax}}% argmax; indices appear below word
\def\argmin{\mathop{\rm argmin}}% argmin; indices appear below word


\graphicspath{{figures/}}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% DATA OF AUTHOR AND DISSERTATION %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\author{Sevket Derin Babacan}

\title{Title of the Dissertation}

%\degree{DOCTOR OF PHILOSOPHY}  % Default: DOCTOR OF PHILOSOPHY

\field{Electrical Engineering and Computer Science}            % Default: Mathematics

%\graduationmonth{June}         % The default is June or December
                                % depending on current date.

%\graduationyear{2003}          % Default: current year.


				% Use \includeonly to select the 
%\includeonly{chap1,chap2,...}	% chapters to include if you are 
				% using the \include command below.
				% This way you can latex only a the 
				% part you are working on, which 
				% is faster than latexing the entire 
				% thesis. 


\begin{document}
%	
%	THE BODY OF YOUR THESIS STARTS HERE
%

%%%%%%%%%%%%%%%%%%%%%%
% Some initial stuff %
%%%%%%%%%%%%%%%%%%%%%%

\frontmatter		% Preliminary pages start here.

\maketitle		% Produces the title page.

\copyrightpage		% Creates the copyright page.


\abstract		% Abstract.

This is the abstract.

\acknowledgements	% Acknowledgements (optional).

Text for acknowledgments.

\preface		% Preface (optional).

This is the preface.



\tableofcontents	% Table of Contents will be automatically
			% generated and placed here.

\listoftables		% List of Tables and List of Figures will be placed
\listoffigures		% here, if applicable (optional).



\mainmatter             % Actual text starts here.

%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Actual text starts here %
%%%%%%%%%%%%%%%%%%%%%%%%%%%

\include{chapter1}

\include{chapter2}

\include{chapter4}
% The command \includeonly above allows to include a selected 
% set of chapters only.

% Uncomment the 'singlespace' environment and '\bibsep' command
% if needed - some bibliographic styles overide the definition
% of 'thebibliography' in nuthesis.cls
%
%\begin{singlespace}
%\bibsep 12pt

\bibliographystyle{IEEEtran}
\bibliography{IEEEabrv,ALLrestoration}


\appendix			% Appendix begins here (optional).

%\appendices			% If more than one appendix chapters,
				% use \appendices instead of \appendix

\chapter{Title of Appendix}	% First appendix chapter, i.e., Appendix A.

\section{First section of Appendix}	% This is appendix section 1.

This is the Appendix.

\subsection{First subsection of Appendix}  % This is appendix subsection 1.

More text ...

\subsubsection{First subsubsection of Appendix}  % This is subsubsection 1.

Yet more text ...


\begin{vita}                    % Vita (optional).

This is the Vita. This is the Vita. This is the Vita. This is the Vita. 
This is the Vita. This is the Vita. This is the Vita. This is the Vita. 
This is the Vita. This is the Vita. This is the Vita. This is the Vita. 
This is the Vita. This is the Vita. This is the Vita. This is the Vita. 

This is the Vita. This is the Vita. This is the Vita. This is the Vita. 
This is the Vita. This is the Vita. This is the Vita. This is the Vita. 
This is the Vita. This is the Vita. This is the Vita. This is the Vita. 
This is the Vita. This is the Vita. This is the Vita. This is the Vita. 

This is the Vita. This is the Vita. This is the Vita. This is the Vita. 
This is the Vita. This is the Vita. This is the Vita. This is the Vita. 
This is the Vita. This is the Vita. This is the Vita. This is the Vita. 
This is the Vita. This is the Vita. This is the Vita. This is the Vita. 


\end{vita}


\end{document}

